A metabolite profiling study has been carried out on Arabidopsis thaliana (L.) Heynh. ecotype Wassilewskija and a series of transgenic lines of the ecotype transformed with a CHS (chalcone synthase) antisense construct. Compound identifications by LC/MS and H-1 NMR are discussed. The glucosinolate composition in rosette leaves was shown to vary naturally within this ecotype. Relatively modest environmental changes had a strong effect on the wild type level of flavonoids and some sinapate esters but much less effect on the glucosinolates. Potentially a reduction in the level of flavonoids could be expected in the transgenic lines relative to the wild type. In practice the reductions achieved were highly variable both between lines and within a given line on different occasions when the plants were grown. Possible reasons for this variability are discussed with reference to current models of gene silencing. The metabolite profiles of the transgenic lines were examined for unintended effects of the modification. An apparently major effect on the glucosinolate composition was shown to result from an unusual genetic variation in the ecotype and not from the modification. The modification did produce a different but much more subtle change in the levels of certain glucosinolates.